{"id":"https://openalex.org/W4405194283","doi":"https://doi.org/10.1038/s42256-024-00946-z","title":"An interpretable RNA foundation model for exploring functional RNA motifs in plants","display_name":"An interpretable RNA foundation model for exploring functional RNA motifs in plants","publication_year":2024,"publication_date":"2024-12-09","ids":{"openalex":"https://openalex.org/W4405194283","doi":"https://doi.org/10.1038/s42256-024-00946-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/39703563"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-024-00946-z","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00946-z","pdf_url":"https://www.nature.com/articles/s42256-024-00946-z.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s42256-024-00946-z.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077790956","display_name":"Haopeng Yu","orcid":"https://orcid.org/0000-0002-5184-2430"},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["CN","GB"],"is_corresponding":true,"raw_author_name":"Haopeng Yu","raw_affiliation_strings":["Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]},{"raw_affiliation_string":"Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100416353","display_name":"Heng Yang","orcid":"https://orcid.org/0000-0002-6831-196X"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Heng Yang","raw_affiliation_strings":["Department of Computer Science, University of Exeter, Exeter, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Exeter, Exeter, UK","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046958117","display_name":"Wenqing Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Wenqing Sun","raw_affiliation_strings":["Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]},{"raw_affiliation_string":"Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055387273","display_name":"Zongyun Yan","orcid":"https://orcid.org/0000-0002-8556-5929"},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I4210112230","display_name":"State Key Laboratory of Plant Genomics","ror":"https://ror.org/0205xz563","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112230"]}],"countries":["CN","GB"],"is_corresponding":false,"raw_author_name":"Zongyun Yan","raw_affiliation_strings":["Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]},{"raw_affiliation_string":"State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210112230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031786281","display_name":"Xiaofei Yang","orcid":"https://orcid.org/0000-0001-5204-1769"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210139738","display_name":"Center for Excellence in Molecular Plant Sciences","ror":"https://ror.org/04ew43640","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210139738"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofei Yang","raw_affiliation_strings":["CAS-JIC Center of Excellence for Plant and Microbial Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China","National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"CAS-JIC Center of Excellence for Plant and Microbial Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210139738","https://openalex.org/I19820366"]},{"raw_affiliation_string":"National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210139738","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075378433","display_name":"Huakun Zhang","orcid":"https://orcid.org/0000-0002-4292-9040"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huakun Zhang","raw_affiliation_strings":["Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086117468","display_name":"Yiliang Ding","orcid":"https://orcid.org/0000-0003-4161-6365"},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Yiliang Ding","raw_affiliation_strings":["Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK"],"affiliations":[{"raw_affiliation_string":"Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100343450","display_name":"Ke Li","orcid":"https://orcid.org/0000-0001-7200-4244"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]},{"id":"https://openalex.org/I4210128584","display_name":"The Alan Turing Institute","ror":"https://ror.org/035dkdb55","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210128584"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ke Li","raw_affiliation_strings":["Alan Turing Institute, London, UK","Department of Computer Science, University of Exeter, Exeter, UK"],"affiliations":[{"raw_affiliation_string":"Alan Turing Institute, London, UK","institution_ids":["https://openalex.org/I4210128584"]},{"raw_affiliation_string":"Department of Computer Science, University of Exeter, Exeter, UK","institution_ids":["https://openalex.org/I23923803"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5077790956"],"corresponding_institution_ids":["https://openalex.org/I100288624","https://openalex.org/I184983240","https://openalex.org/I2799300731"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":6.843,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.97821043,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"6","issue":"12","first_page":"1616","last_page":"1625"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.7961497902870178},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7076754570007324},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5441227555274963},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5157535076141357},{"id":"https://openalex.org/keywords/nucleic-acid-structure","display_name":"Nucleic acid structure","score":0.5133268237113953},{"id":"https://openalex.org/keywords/riboswitch","display_name":"Riboswitch","score":0.4716555178165436},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.4047289192676544},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2516895532608032},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23683136701583862},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1975829303264618}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7961497902870178},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7076754570007324},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5441227555274963},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5157535076141357},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.5133268237113953},{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.4716555178165436},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.4047289192676544},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2516895532608032},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23683136701583862},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1975829303264618}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1038/s42256-024-00946-z","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00946-z","pdf_url":"https://www.nature.com/articles/s42256-024-00946-z.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},{"id":"pmid:39703563","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39703563","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature machine intelligence","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11652376","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11652376","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11652376/pdf/42256_2024_Article_946.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Mach Intell","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1038/s42256-024-00946-z","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00946-z","pdf_url":"https://www.nature.com/articles/s42256-024-00946-z.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6700000166893005,"display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1426318481","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G1752709255","display_name":null,"funder_award_id":"2412023YQ005","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2041897690","display_name":null,"funder_award_id":"2023YFA0913500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2615012307","display_name":null,"funder_award_id":"62076056","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2679502546","display_name":null,"funder_award_id":"MR/X011135/1","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"},{"id":"https://openalex.org/G3207946773","display_name":null,"funder_award_id":"3210022","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6154587524","display_name":null,"funder_award_id":"00221","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G6209149755","display_name":null,"funder_award_id":"BBS/E/JI/230002A","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G6574541588","display_name":null,"funder_award_id":"2021YFF1000900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6708675553","display_name":null,"funder_award_id":"MR/S017062/1","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"},{"id":"https://openalex.org/G6861406334","display_name":null,"funder_award_id":"202206","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8126170492","display_name":null,"funder_award_id":"202206","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8238418921","display_name":null,"funder_award_id":"BB/X01102X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8245872083","display_name":null,"funder_award_id":"62376056","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8337499222","display_name":null,"funder_award_id":"BBS/E/JI/230002B","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8589651859","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G8591886698","display_name":null,"funder_award_id":"BB/X01102X","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G8951484681","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405194283.pdf","grobid_xml":"https://content.openalex.org/works/W4405194283.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1964813963","https://openalex.org/W2017313617","https://openalex.org/W2032698727","https://openalex.org/W2041882488","https://openalex.org/W2049661143","https://openalex.org/W2062299199","https://openalex.org/W2074613554","https://openalex.org/W2076091642","https://openalex.org/W2086561953","https://openalex.org/W2100908594","https://openalex.org/W2102278945","https://openalex.org/W2123467717","https://openalex.org/W2141292707","https://openalex.org/W2170747616","https://openalex.org/W2179438025","https://openalex.org/W2528320810","https://openalex.org/W2536860838","https://openalex.org/W2558189049","https://openalex.org/W2759571676","https://openalex.org/W2762224301","https://openalex.org/W2770378609","https://openalex.org/W2785610594","https://openalex.org/W2801727539","https://openalex.org/W2951298881","https://openalex.org/W2981543307","https://openalex.org/W3041336634","https://openalex.org/W3045414875","https://openalex.org/W3111554733","https://openalex.org/W3143154750","https://openalex.org/W3162971530","https://openalex.org/W3177828909","https://openalex.org/W3180908419","https://openalex.org/W3216115362","https://openalex.org/W4213095938","https://openalex.org/W4283072263","https://openalex.org/W4292121948","https://openalex.org/W4306353420","https://openalex.org/W4306882669","https://openalex.org/W4312197262","https://openalex.org/W4316339774","https://openalex.org/W4327550249","https://openalex.org/W4378385554","https://openalex.org/W4382490702","https://openalex.org/W4383956555","https://openalex.org/W4386811611","https://openalex.org/W4388717695","https://openalex.org/W4388979610","https://openalex.org/W4392150844","https://openalex.org/W4393981110","https://openalex.org/W4394763992","https://openalex.org/W6954761648"],"related_works":["https://openalex.org/W1472344963","https://openalex.org/W3170509043","https://openalex.org/W3093937951","https://openalex.org/W2554722417","https://openalex.org/W2470187006","https://openalex.org/W2058984380","https://openalex.org/W1988125422","https://openalex.org/W4247914012","https://openalex.org/W2116507553","https://openalex.org/W2581348958"],"abstract_inverted_index":{"The":[0],"complex":[1,40],"'language'":[2,41],"of":[3,10,18,92,117,151,155,170,177],"plant":[4,19,77,180],"RNA":[5,54,68,71,120,127,141,158,172,186],"encodes":[6],"a":[7,50],"vast":[8],"array":[9],"biological":[11],"regulatory":[12],"elements":[13],"that":[14,113],"orchestrate":[15],"crucial":[16],"aspects":[17],"growth,":[20],"development":[21],"and":[22,52,70,122,129],"adaptation":[23],"to":[24,38],"environmental":[25],"stresses.":[26],"Recent":[27],"advancements":[28],"in":[29,42,83,143,160,188],"foundation":[30],"models":[31],"(FMs)":[32],"have":[33],"demonstrated":[34],"their":[35],"unprecedented":[36],"potential":[37],"decipher":[39],"biology.":[43],"In":[44],"this":[45],"study,":[46],"we":[47,138],"introduced":[48],"PlantRNA-FM,":[49],"high-performance":[51],"interpretable":[53,111],"FM":[55],"specifically":[56],"designed":[57],"for":[58,94,184],"plants.":[59,144,189],"PlantRNA-FM":[60,79,87,106,146,166],"was":[61],"pretrained":[62],"on":[63],"an":[64,89],"extensive":[65],"dataset,":[66],"integrating":[67],"sequences":[69],"structure":[72,123,131],"information":[73,154],"from":[74],"1,124":[75],"distinct":[76],"species.":[78],"exhibits":[80],"superior":[81],"performance":[82],"plant-specific":[84],"downstream":[85],"tasks.":[86],"achieves":[88,103],"F1":[90],"score":[91],"0.974":[93],"genic":[95,161],"region":[96],"annotation,":[97],"whereas":[98],"the":[99,115,149,152,168,175],"current":[100],"best-performing":[101],"model":[102],"0.639.":[104],"Our":[105,145],"is":[107],"empowered":[108],"by":[109],"our":[110,165],"framework":[112],"facilitates":[114,167],"identification":[116],"biologically":[118],"functional":[119,157,171],"sequence":[121],"motifs,":[124],"including":[125],"both":[126],"secondary":[128],"tertiary":[130],"motifs":[132,142,159,173],"across":[133,174],"transcriptomes.":[134],"Through":[135],"experimental":[136],"validations,":[137],"revealed":[139],"translation-associated":[140],"also":[147],"highlighted":[148],"importance":[150],"position":[153],"these":[156],"regions.":[162],"Taken":[163],"together,":[164],"exploration":[169],"complexity":[176],"transcriptomes,":[178],"empowering":[179],"scientists":[181],"with":[182],"capabilities":[183],"programming":[185],"codes":[187]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":19}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
